Solution Structure of the HOIL-1L NZF Domain Reveals a Conformational Switch Regulating Linear Ubiquitin Affinity

Overview

Journal J Biol Chem

Specialty Biochemistry

Date 2023 Aug 18

PMID 37595872

Authors

Erik Walinda

Kenji Sugase

Naoki Ishii

Masahiro Shirakawa

Kazuhiro Iwai

Daichi Morimoto

Affiliations

Soon will be listed here.

Abstract

Attachment of polyubiquitin (poly-Ub) chains to proteins is a major posttranslational modification in eukaryotes. Linear ubiquitin chain assembly complex, consisting of HOIP (HOIL-1-interacting protein), HOIL-1L (heme-oxidized IRP2 Ub ligase 1), and SHARPIN (Shank-associated RH domain-interacting protein), specifically synthesizes "head-to-tail" poly-Ub chains, which are linked via the N-terminal methionine α-amino and C-terminal carboxylate of adjacent Ub units and are thus commonly called "linear" poly-Ub chains. Linear ubiquitin chain assembly complex-assembled linear poly-Ub chains play key roles in immune signaling and suppression of cell death and have been associated with immune diseases and cancer; HOIL-1L is one of the proteins known to selectively bind linear poly-Ub via its Npl4 zinc finger (NZF) domain. Although the structure of the bound form of the HOIL-1L NZF domain with linear di-Ub is known, several aspects of the recognition specificity remain unexplained. Here, we show using NMR and orthogonal biophysical methods, how the NZF domain evolves from a free to the specific linear di-Ub-bound state while rejecting other potential Ub species after weak initial binding. The solution structure of the free NZF domain revealed changes in conformational stability upon linear Ub binding, and interactions between the NZF core and tail revealed conserved electrostatic contacts, which were sensitive to charge modulation at a reported phosphorylation site: threonine-207. Phosphomimetic mutations reduced linear Ub affinity by weakening the integrity of the linear di-Ub-bound conformation. The described molecular determinants of linear di-Ub binding provide insight into the dynamic aspects of the Ub code and the NZF domain's role in full-length HOIL-1L.

References

Skora L, Mestan J, Fabbro D, Jahnke W, Grzesiek S . NMR reveals the allosteric opening and closing of Abelson tyrosine kinase by ATP-site and myristoyl pocket inhibitors. Proc Natl Acad Sci U S A. 2013; 110(47):E4437-45. PMC: 3839726. DOI: 10.1073/pnas.1314712110. View

Tokunaga F, Nishimasu H, Ishitani R, Goto E, Noguchi T, Mio K . Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation. EMBO J. 2012; 31(19):3856-70. PMC: 3463848. DOI: 10.1038/emboj.2012.241. View

Bansal M, Kumar S, Velavan R . HELANAL: a program to characterize helix geometry in proteins. J Biomol Struct Dyn. 2000; 17(5):811-9. DOI: 10.1080/07391102.2000.10506570. View

Krissinel E, Henrick K . Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372(3):774-97. DOI: 10.1016/j.jmb.2007.05.022. View

Wang B, Alam S, Meyer H, Payne M, Stemmler T, Davis D . Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. J Biol Chem. 2003; 278(22):20225-34. PMC: 3366119. DOI: 10.1074/jbc.M300459200. View

Kirisako T, Kamei K, Murata S, Kato M, Fukumoto H, Kanie M . A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J. 2006; 25(20):4877-87. PMC: 1618115. DOI: 10.1038/sj.emboj.7601360. View

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

Ikeda F, Deribe Y, Skanland S, Stieglitz B, Grabbe C, Franz-Wachtel M . SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis. Nature. 2011; 471(7340):637-41. PMC: 3085511. DOI: 10.1038/nature09814. View

Sato Y, Fujita H, Yoshikawa A, Yamashita M, Yamagata A, Kaiser S . Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc Natl Acad Sci U S A. 2011; 108(51):20520-5. PMC: 3251058. DOI: 10.1073/pnas.1109088108. View

10.

Valafar H, Prestegard J . REDCAT: a residual dipolar coupling analysis tool. J Magn Reson. 2004; 167(2):228-41. DOI: 10.1016/j.jmr.2003.12.012. View

11.

Stieglitz B, Rana R, Koliopoulos M, Morris-Davies A, Schaeffer V, Christodoulou E . Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature. 2013; 503(7476):422-426. PMC: 3838313. DOI: 10.1038/nature12638. View

12.

Vranken W, Boucher W, Stevens T, Fogh R, Pajon A, Llinas M . The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins. 2005; 59(4):687-96. DOI: 10.1002/prot.20449. View

13.

Lo Y, Lin S, Rospigliosi C, Conze D, Wu C, Ashwell J . Structural basis for recognition of diubiquitins by NEMO. Mol Cell. 2009; 33(5):602-15. PMC: 2749619. DOI: 10.1016/j.molcel.2009.01.012. View

14.

Ye Y, Blaser G, Horrocks M, Ruedas-Rama M, Ibrahim S, Zhukov A . Ubiquitin chain conformation regulates recognition and activity of interacting proteins. Nature. 2012; 492(7428):266-70. PMC: 3605796. DOI: 10.1038/nature11722. View

15.

Johnson B, Blevins R . NMR View: A computer program for the visualization and analysis of NMR data. J Biomol NMR. 2012; 4(5):603-14. DOI: 10.1007/BF00404272. View

16.

Sugase K, Dyson H, Wright P . Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature. 2007; 447(7147):1021-5. DOI: 10.1038/nature05858. View

17.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

18.

Morimoto D, Walinda E, Iwakawa N, Nishizawa M, Kawata Y, Yamamoto A . High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies. Anal Chem. 2017; 89(14):7286-7290. DOI: 10.1021/acs.analchem.7b01816. View

19.

Tokunaga F, Nakagawa T, Nakahara M, Saeki Y, Taniguchi M, Sakata S . SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex. Nature. 2011; 471(7340):633-6. DOI: 10.1038/nature09815. View

20.

Liu Z, Gong Z, Cao Y, Ding Y, Dong M, Lu Y . Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques. Biochemistry. 2017; 57(3):305-313. DOI: 10.1021/acs.biochem.7b00817. View